Well it depends.
Leonardo is the best Ninja; he's the most dedicated and serious about it, and he is the master of turtle combat.
Michaelangelo is the best in that he's the fastest and has the most potential. Too bad he's got pizza and reporters on the brain.
Donatello is the best because he's the most perceptive and cautious, and he only needs one weapon.
Raphael is the best because he's got the most willpower. His anger may be a disadvantage, but he makes up for it with his never die attitude.